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In what appears to be the first mainstream admission that the Swine Flu might well be of human creation, Bloomberg reports on an Australian researcher (a plant virologist) who suspects that the infection may have arisen from a vaccination laboratory, by mistake of course:

[Emeritus Professor] Adrian Gibbs, 75, who collaborated on research that led to the development of Roche Holding AG’s Tamiflu drug, said in an interview that he intends to publish a report suggesting the new strain may have accidentally evolved in eggs scientists use to grow viruses and drugmakers use to make vaccines. Gibbs said he came to his conclusion as part of an effort to trace the virus’s origins by analyzing its genetic blueprint.

A similar theory existed for Avian influenza. That is, that it leaked from a laboratory in China by mistake (of course), possibly from a biological weapons laboratory. For those out there who had some kind of notion that nobody was developing biological weapons anymore, then you ought to surf Google more!

Yes, this virus strain could be a case of mistaken release of a partially attenuated pathogen, but what, pray tell, are supposedly legitimate pharmaecutical companies doing with these unusual and, dare we suggest, practically off-limits viral RNA in their possession? Why did this virus start off in pigs in Mexico?

We discussed earlier how the theory that this virus is natural is an implausible one, that three viral strains (as originally reported) do not simply combine in vivo without leaving a very obvious train of precursor strains. We also discussed, jokingly, how the virus outbreak may have been no mistake (something that requires constant consideration, as there are many plausible motives). The facts are now beginning to fall into place, but this most intriguing of mysteries is still not close to being solved.

Swine flu has infected 5,251 people in 30 countries so far, killing 61, according to the WHO. Scientists are trying to determine whether the virus will mutate and become more deadly if it spreads to the Southern Hemisphere and back.

So far the mortality rate stands at 0.6%, which is nowhere near that of Spanish Flu, and is roughly equal to the annual death rate in Australia. That’s actually a lot of deaths, but still nothing to be particularly worried about. It needs to be borne in mind that most of the deaths occurred in Mexico, which does not have the same underlying health, demographics and climate as most of the developed world. Update: 17/5/09 – It is estimated that more than 100,000 infections have occurred in the U.S, and given the death rate so far.

If Dr. Gibbs is correct, which it appears he is, then it should be possible to find out exactly which laboratory produced the pathogen. Possible, of course, does not mean easy. Those working in biological research laboratories, especially those working with dangerous organisms, are in a particularly vulnerable situation. Not only do they need to be very careful how they handle the microbes, but they must take special care with the information they collect and be mindful as to how that information is likely to be used. No profession is without ethical dilemmas.

Bloomberg’s article goes on:

In addition, his research found the rate of genetic mutation in the new virus outpaced that of the most closely related viruses found in pigs, suggesting it evolved outside of swine, Gibbs said. Some scientists have speculated that the 1977 Russian flu, the most recent global outbreak, began when a virus escaped from a laboratory.

…

Gibbs said he has no evidence that the swine-derived virus was a deliberate, man-made product.

“I don’t think it could be a malignant thing,” he said. “It’s much more likely that some random thing has put these two viruses together.”

Well, everybody is innocent until proven guilty. It is also quite correct to say that this virus is unlikely to be a biological weapon, because its lethality is so low. Nonetheless, this virus has the potential to cause as much death and morbidity as did the Chernobyl reactor disaster of 1986 – an event that partly triggered the collapse of the Soviet Union. Should the origins of this virus turn out to be one of an established superpower, or an emerging one, it could well spur some seizmic shifts on a political level.

The Swine Flu has been covered ad nauseam in the media, with many aspects addressed, however little has been elucidated on the first (and most important) question I had when this strain broke loose:

How can three virus strains combine, in nature, to form a single, viable virus?

To answer this question we need to look at a little bit of background information on the Influenza A virus (in brief). It is an RNA virus, a genus of the Orthomyxoviridae family. The virus itself lacks most of the needed equipment (enzymes and so forth) for replication and depends on the body’s own cells, which it enters on contact with outer membranes. The protective viral coat breaks open inside the cell, with the RNA being fed to the cell’s protein making “factories” to reproduce the viral coat which protects the virus and enables its further spread, and also the enzymes necessary to replicate the virus’ RNA (RNA Polymerase). The completed virus particle either continues to reproduce inside the cell, or is expelled by the cell itself, where, if successful, it survives long enough to infect another cell.

The replication process itself is very error prone (much more so than that for human DNA), such that many of the viral copies fail. Some errors work, however. This may result in a more “successful” viral particle. This system of natural selection means that, over time (sometimes a very short time), a virus adapts to its host, which can be a good or bad thing:

The virus might develop a slower replication rate, so that the symptom free phase is longer, allowing it to spread to more hosts. This would make it a better virus than one which kills its host so quickly that it has never had a chance to spread to a new host.

The virus might develop into a more benign form, so that it can spread happily without the host minding too much. This could be an advantage for the virus, for example, if the sickest individuals were quarantined (or dead), rendering that viral trait undesirable and selecting for less severe traits.

The virus might develop into one which can survive a longer time in the atmosphere, increasing its infectiousness. It could be said that the universal wearing of surgical masks, for example, might mean that the virus will be pressured into learning how to spread in more extreme conditions (past the mask), making it more virulent.

Many of the symptoms of flu virus are deliberate, such as mucous membrane irritation which causes people to sneeze and cough, or develop diarrhoea. These aide the spread of the virus, which is why hand washing and the wearing of masks is advocated by authorities. On the other hand, measures to stop the virus can promote a super-strain which can make matters worse.

The important point, to answer the question, is that the Viral RNA is not presented as a single strand but, in the case of Influenza, eight separate segments. These float around near the nucleus of the cell relatively freely until they are repackaged. Thus, it is possible (either in a laboratory or in nature) for a cell to be infected by two different virus strains simultaneously, resulting in any number of random combinations of the Viral RNA segments, any of which may potentially result in a successful virus particle. Most of the time, however, it can be expected that recombinations would fail.

The combination of two virus strains can easily occur in nature. Three is less likely.

However, it should take a long time for three viruses to combine into one coat. Long enough for a precursor to have spread widely, causing animals to get sick so that they get tested, perhaps to the point that the new genome is detected in a laboratory, before a third virus is incorporated into the new strain. It should also be possible to find a virus having a combination of two of the three RNA strains somewhere else in the wild. This may have occurred already in pigs in Ohio (2007). There are doubts, however, that the Ohio outbreak is not a red herring, as is covered well here.

Yet it is now reported by wired magazine that the viral genome is entirely made up of elements from pigs only and only from two, pre-existent strains, a claim that needs further corroboration. But if this is true, then the almost-pandemic A/H1N1 virus can safely be viewed as one having developed entirely naturally, but precursors still need to be found.

Swine Flu A Natural Occurrence?

The current outbreak of Swine Flu is probably a natural occurrence, but the work necessary to show this is incomplete. The question, as at 1/5/2009, remains unanswered, and thus, the theory that the outbreak was no accident, cannot yet be discounted as just another of the flighty ideas of a paranoid lunatic.

(As this stage, we won’t be covering any more of this epidemic, unless something new and meaningful is learned of the virus itself. Instead, we intend on concentrating on other, more pressing matters.)

Health alerts have spread through Australia’s government institutions, in particular hospitals, advising of the risk of Swine Flu. It affects young adults, has a high probability of mortality, and is described by the World Health Organization as an emergency having the potential to reach pandemic proportions rapidly. In Mexico, it is said that over 1000 people at the present time have been infected, of which over 60 (27/4/09 – now 80) have died – a fatality rate of (roughly) 6%. Schools, museums and other public gathering places have been closed to try to prevent further spread. The virus has already spread to California, Texas, with at least seven confirmed infections.

The number of fatalities outside of Mexico currently equals 1, a 23 month old in the US.

Specifically, the virus belongs to the H1N1 group of influenza A viruses. This particular strain is novel; its discovery occurred as recently as 2 days ago (23/4/2009). Its genetic profile is such that the conventional flu vaccines offered to hospital workers and the community are unlikely to offer protection. It is said to be sensitive to the drugs zanamivir (Relenza, owned by GSK) and oseltamivir (Tamiflu, owned by Roche). Supplies of this drug in Australia are probably adequate to manage the early stages of an outbreak, but clearly, in developing countries, this is definitely not the case.

The lethality of this infection is similar to that during the Spanish Flu pandemic (1918-1920) which had a mortality rate of 2 to 20%. It too was a subtype of the H1N1 influenza A virus.

One of the most common questions being asked by the public are about the presentation of the illness and how to avoid getting infected. In general, the symptoms and signs of the infection are nothing out of the ordinary. They include:

All the usual flu symptoms, such as fever, lethargy, lack of appetite and coughing (respiratory tract), sometimes runny nose and sore throat.

Other body systems can also be involved, such the gut (nausea and vomiting, diarrhoea)

These are the same symptoms that can happen in pneumonia, the common cold, even urinary tract infection in some people. This is not very helpful, because it can now be expected that, very often, a person with even the slightest runny nose, or food poisoning or whatever, will think he or she has swine flu. The rule of thumb is, if you are more sick than your usual, see a doctor. If you have a reason to avoid being sick at all (such as being on drugs which decrease your immunity), see a doctor.

As for avoiding infection, well there are more myths than facts around. If you managed to avoid catching a cold over the last five years, then you are doing something right, but the fact is that most people are forced to go to public places, shop, go to school, work and so forth. Like every virus, the flu will have an incubation period (even if it’s just a couple of days) where a person is infected, is infectious, but is feeling perfectly well.

Of the few things that have been proven to work, careful and consistent hand washing after human contact, isolation of the sick, vaccines (by no means a panacea), and being otherwise healthy, well slept and well fed, are the best thing. If you are worried about dying, but smoke, drink too much, go to fast food restaurants and drive too fast, then fix those before you worry about the flu!

The coming weeks will reveal whether this virus manages to spread faster than the ability of researchers to design a vaccine in order to produce herd immunity, especially in major cities. In the meantime, governments around the world will be placing their institutions on alert for symptoms and putting in place treatment protocols and the like. There is no doubt that everybody will do whatever is feasible to curtail the spread of this organism.

The flu virus mutates promiscuously, and this strain is no exception: Officials said that, in addition to genetic material associated with North American swine flu, the strain has gene segments associated with European and Asian swine flu, North American avian flu and human flu.

Most surgical masks do not offer protection.

Three strains in one! It’s not unreasonable to ask questions about just how probable (or improbable) such a mutation is in the wild. In laboratories, however, mixtures of multiple viral RNA fragments can be combined to yield a successful result. Biological weapons research has not ceased either, but has continued quietly out of the public limelight. We can expect to hear of many different explanations about this particular virus.

It is useful to keep an open mind about the outbreak. It is currently assumed that the virus is a natural occurrence. Indeed, there have been warnings about this for years now. The thing is, though, that warnings do not change the probabilities. Many people are rightly wondering whether the virus was engineered in a laboratory or is merely a coincidental mutation among a herd of pigs. If it is a man-made virus, then its release into the wild could represent the greatest act of mass murder in history. This question, therefore, is not to be shirked at and must be answered.

The influenza viruses, however, are known for their unstable genetics and rapid rate of mutation, hence the tendency for new strains to emerge each year, and even during a seasonal outbreak. It would be interesting to tease out the probabilities that this particular strain would have spontaneously emerged. Also, we can expect this outbreak, if it does spread as predicted, to rapidly mutate into multiple strains, making containment even more difficult.

On the topic of containment, it needs to be said that ordinary surgical masks do little to prevent the spread of influenza. It’s all just for show. During the first few minutes of wearing a surgical mask, the device performs to manufacturer specifications, but after that the mask is damp and warm and cannot offer the same protection. A paper mask cannot form a tight seal around the face so that air is always entrained on inhalation. If you are sneezed on, or are in contact with an infected person, you are going to get infected. Mask wearing is by and large a waste of time – as good as placebo. But people will do it anyway, of course.

Whatever its origins, this virus is already showing an ability to spread extremely rapidly. Within days we will know whether this is indeed the flu pandemic of the century.